Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011264.1 Kokia drynarioides strain JFW-HI SEQ_126243, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57166
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:1406 original size:29 final size:30
Alignment explanation
Indices: 1341--1417 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
1331 ATACCAAAAC
* *
1341 TATACATGAACTATGGTTTAATGTACAATTG
1 TATACATGAACTTTGATTT-ATGTACAATTG
* *
1372 CATACATGAACTTTGATTT-TGTGCAATTG
1 TATACATGAACTTTGATTTATGTACAATTG
1401 TATACATGAA--TTGATTT
1 TATACATGAACTTTGATTT
1418 GATTCAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.17
29 18 0.44
31 16 0.39
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTACAATTG
Found at i:3805 original size:21 final size:21
Alignment explanation
Indices: 3771--3810 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3761 TTTATCACAT
* * *
3771 AATAAATTACATATCATATAA
1 AATAAAATAAATATAATATAA
3792 AATAAAATAAATATAATAT
1 AATAAAATAAATATAATAT
3811 GTCATATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAAATAAATATAATATAA
Found at i:12529 original size:18 final size:17
Alignment explanation
Indices: 12494--12533 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
12484 TTCAATGCAG
*
12494 TATT-TAATTTTTATTT
1 TATTATAATTTTAATTT
12510 TATTATAATGTTTAATTT
1 TATTATAAT-TTTAATTT
12528 TATTAT
1 TATTAT
12534 CACAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTATAATTTTAATTT
Found at i:13858 original size:21 final size:21
Alignment explanation
Indices: 13828--13871 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13818 CACATCCATG
13828 AATAATAATTATAT-CACATA
1 AATAATAATTATATCCACATA
*
13848 AATACATAATTTTATCCACATA
1 AATA-ATAATTATATCCACATA
13870 AA
1 AA
13872 ATATACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAATAATTATATCCACATA
Found at i:14440 original size:14 final size:14
Alignment explanation
Indices: 14421--14457 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14411 GTCGACATCC
14421 TTTTTTTGTCAAAT
1 TTTTTTTGTCAAAT
*
14435 TTTTTTTTTCAAAT
1 TTTTTTTGTCAAAT
*
14449 TTTGTTTGT
1 TTTTTTTGT
14458 GTTGGCCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.70
Consensus pattern (14 bp):
TTTTTTTGTCAAAT
Found at i:14646 original size:57 final size:58
Alignment explanation
Indices: 14506--14647 Score: 134
Period size: 57 Copynumber: 2.5 Consensus size: 58
14496 AAAGGAATGG
*
14506 CAACACAAAAAAATTTTGAAATTTTTTTCTTAAAAAGGAGGCGTCGGCCATGCAATGAC
1 CAACACAAAAAAATTCTGAAA-TTTTTTCTTAAAAAGGAGGCGTCGGCCATGCAATGAC
* * * ** *
14565 CAACACCCAAAAAA--GT-AATTTTTTTTCTTAAAAAGTTGGTGTC-GCCATTGC-AT-AGC
1 CAACA-CAAAAAAATTCTGAA-ATTTTTTCTTAAAAAGGAGGCGTCGGCCA-TGCAATGA-C
14621 CAACACAAAAAAATTCTGAAATTTTTT
1 CAACACAAAAAAATTCTGAAATTTTTT
14648 TTTTGACAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
55 8 0.12
56 12 0.18
57 32 0.48
58 3 0.04
59 5 0.07
60 7 0.10
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (58 bp):
CAACACAAAAAAATTCTGAAATTTTTTCTTAAAAAGGAGGCGTCGGCCATGCAATGAC
Found at i:15635 original size:16 final size:15
Alignment explanation
Indices: 15614--15643 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15604 AGGAAAGAAA
15614 GAAGAAGGAAGAAGGG
1 GAAGAAGG-AGAAGGG
15630 GAAGAAGGAGAAGG
1 GAAGAAGGAGAAGG
15644 AAAAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGG
Found at i:16016 original size:21 final size:20
Alignment explanation
Indices: 15990--16032 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
15980 TAATTCACTT
15990 TAATTTAACTTTGTTAGTTAG
1 TAATTTAACTTTGTT-GTTAG
* *
16011 TAATTTTATTTTGTTGTTAG
1 TAATTTAACTTTGTTGTTAG
16031 TA
1 TA
16033 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (20 bp):
TAATTTAACTTTGTTGTTAG
Found at i:16294 original size:30 final size:30
Alignment explanation
Indices: 16258--16364 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
16248 TAAACTTGGC
*
16258 TAATTAATTTTCAAAATATAATATACAAAA
1 TAATTAATTATCAAAATATAATATACAAAA
***
16288 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTATCAAAATATAATATACAAAA
*
16315 TCATATT-ATTGACCAAAATATAATATACAAAA
1 T-A-ATTAATT-ATCAAAATATAATATACAAAA
16347 TAATTAATTATCAAAATA
1 TAATTAATTATCAAAATA
16365 ATATCCCCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
27 3 0.05
28 11 0.18
29 8 0.13
30 25 0.41
31 11 0.18
32 3 0.05
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (30 bp):
TAATTAATTATCAAAATATAATATACAAAA
Found at i:16302 original size:16 final size:16
Alignment explanation
Indices: 16258--16307 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
16248 TAAACTTGGC
*
16258 TAATTAATTTTCAAAA
1 TAATTAATTATCAAAA
16274 T-A-TAA-TATACAAAA
1 TAATTAATTAT-CAAAA
16288 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
16304 TAAT
1 TAAT
16308 ATCCCCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 2 0.07
16 13 0.45
17 3 0.10
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:16332 original size:59 final size:59
Alignment explanation
Indices: 16269--16383 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
16259 AATTAATTTT
16269 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
1 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
*
16328 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATTTTATT
1 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATT
16384 TTGTTGTTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (59 bp):
CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
Found at i:16857 original size:22 final size:22
Alignment explanation
Indices: 16829--16873 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16819 TGTACTATTT
16829 TAGTAAATAACACATTTTGGTA
1 TAGTAAATAACACATTTTGGTA
*
16851 TAGTAAATAACATATTTTGGTA
1 TAGTAAATAACACATTTTGGTA
16873 T
1 T
16874 TTAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (22 bp):
TAGTAAATAACACATTTTGGTA
Found at i:18251 original size:45 final size:45
Alignment explanation
Indices: 18187--18322 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 45
18177 GCATAGCTCA
18187 TAAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TAAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
18232 TAAAACCAAGGATATCAGCCTCAATTTGACGAGCAACCGCAATAC
1 TAAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *** * * * *
18277 TCAATGGAAGGATATCAGGCTGAGTTTGACGCGTCACCGCAATAC
1 TAAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
18322 T
1 T
18323 CTATTCCTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (45 bp):
TAAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:18341 original size:21 final size:21
Alignment explanation
Indices: 18315--18360 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
18305 ACGCGTCACC
*
18315 GCAATACTCTATTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
18336 GCAATACTCTACTCCTCCTGG
1 GCAATACTCTACTCCTCCCGG
18357 GCAA
1 GCAA
18361 ATGGACCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:21940 original size:4 final size:4
Alignment explanation
Indices: 21933--21988 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
21923 ATACATTACT
* * * * *
21933 TTTC TTTC CTTC -TTC TTTC TTTTC TCTC ATTC TTCC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC
21981 TTTC TTTC
1 TTTC TTTC
21989 CCGTTTATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 3 0.07
4 36 0.84
5 4 0.09
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:21956 original size:20 final size:20
Alignment explanation
Indices: 21931--21986 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
21921 AAATACATTA
* *
21931 CTTTTCTTTCCTTCTTCTTT
1 CTTTTCTTTCATTCTTCCTT
*
21951 CTTTTCTCTCATTCTTCCTT
1 CTTTTCTTTCATTCTTCCTT
* *
21971 CCTTTCTTTCTTTCTT
1 CTTTTCTTTCATTCTT
21987 TCCCGTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTCTTTCATTCTTCCTT
Found at i:32650 original size:8 final size:8
Alignment explanation
Indices: 32635--32673 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
32625 TTTCATGTAA
32635 TCATTTCT
1 TCATTTCT
*
32643 TCACTTCT
1 TCATTTCT
32651 TCATTTCT
1 TCATTTCT
32659 TCATTTCT
1 TCATTTCT
32667 TCATTTC
1 TCATTTC
32674 CCACGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (8 bp):
TCATTTCT
Found at i:55240 original size:70 final size:67
Alignment explanation
Indices: 55150--55282 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
55140 TCCGAATAAG
* * * *
55150 AAAAGGTAAAATTACATCATTTTGATAAATTTTTATCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAAGTAAAATTACATCATTTTGATAAATGTTTATCC-AT-T-AAGTTAAAAGGCAAAACCATT
55215 AAGTT
63 AAGTT
** *
55220 AAAAAGTAAAATTATGTCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACTATTA
1 AAAAAGTAAAATTACATCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACCATTA
55283 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 20 0.36
68 1 0.02
69 1 0.02
70 34 0.61
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (67 bp):
AAAAAGTAAAATTACATCATTTTGATAAATGTTTATCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:56952 original size:412 final size:412
Alignment explanation
Indices: 56188--57166 Score: 1832
Period size: 412 Copynumber: 2.4 Consensus size: 412
56178 CGCGGACACG
* * * *
56188 TTCTTCGACACGACGTTCAAGAAGAAGATACGAAAATAGATTATAACAATCAATTTCTGTGGAAT
1 TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
* * *
56253 CGATCCTACTGTCTTATACTACTATTTTATATTATTTTACTATAAAATTACTTATATTTGGTGAA
66 CGATCCTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
* *
56318 TTCAACGCCCATTATTTATCCAATTTCTCGAAAGATGATACATCAAAAATTAATTTGAAAGATCC
131 TTCAACGCCCATCATTTATCCAAATTCTCGAAAGATGATACATCAAAAATTAATTTGAAAGATCC
* *
56383 AGTGGAGGGAGTTTCCATAGAACTGAAACAAATTCTGAAAAGTTAAGATTTTTCATAGGGGGAAA
196 AGTGGAGGGAGTTTCCATAGAACTGAAACAAATTCTGAAAAGTTAAGATTCTTCACAGGGGGAAA
*
56448 GAGCAGAAAATTACACACCCCAGGATTATTCGTTGCACAAAACCACGCAAAGGTCTAGTCAACAC
261 GAGCAGAAAATTACACACACCAGGATTATTCGTTGCACAAAACCACGCAAAGGTCTAGTCAACAC
56513 AAGCAAATTTCCCATAGGGCGAAAACGAAAGACAATGAACCAGTGAATTGATGGATGGTGGACCC
326 AAGCAAATTTCCCATAGGGCGAAAACGAAAGACAATGAACCAGTGAATTGATGGATGGTGGACCC
56578 ACTCCTTTGGGGTGACATTATC
391 ACTCCTTTGGGGTGACATTATC
56600 TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
1 TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
56665 CGATCCTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
66 CGATCCTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
56730 TTCAACGCCCATCATTTATCCAAATTCTCGAAAGATGATACATCAAAAATTAATTTGAAAGATCC
131 TTCAACGCCCATCATTTATCCAAATTCTCGAAAGATGATACATCAAAAATTAATTTGAAAGATCC
*
56795 AGTGGAGGGAGTTTCCATAGAACTGAAACAAATTCTGAAAAGTTGAGATTCTTCACAGGGGGAAA
196 AGTGGAGGGAGTTTCCATAGAACTGAAACAAATTCTGAAAAGTTAAGATTCTTCACAGGGGGAAA
56860 GAGCAGAAAATTACACACACCAGGATTATTCGTTGCACAAAACCACGCAAAGGTCTAGTCAACAC
261 GAGCAGAAAATTACACACACCAGGATTATTCGTTGCACAAAACCACGCAAAGGTCTAGTCAACAC
56925 AAGCAAATTTCCCATAGGGCGAAAACGAAAGACAATGAACCAGTGAATTGATGGATGGTGGACCC
326 AAGCAAATTTCCCATAGGGCGAAAACGAAAGACAATGAACCAGTGAATTGATGGATGGTGGACCC
56990 ACTCCTTTGGGGTGACATTATC
391 ACTCCTTTGGGGTGACATTATC
57012 TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
1 TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
*
57077 CGATCTTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
66 CGATCCTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
57142 TTCAACGCCCATCATTTATCCAAAT
131 TTCAACGCCCATCATTTATCCAAAT
Statistics
Matches: 553, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
412 553 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (412 bp):
TTCTTCGACACGACATTCAAGAAAAAGATACGAAAATAAATTACAACAATCAATTTCTGTGGAAT
CGATCCTACTGTCTTATATTATTATTTTATATTATTTTACCATAAAATTACTTATATTTGGTGAA
TTCAACGCCCATCATTTATCCAAATTCTCGAAAGATGATACATCAAAAATTAATTTGAAAGATCC
AGTGGAGGGAGTTTCCATAGAACTGAAACAAATTCTGAAAAGTTAAGATTCTTCACAGGGGGAAA
GAGCAGAAAATTACACACACCAGGATTATTCGTTGCACAAAACCACGCAAAGGTCTAGTCAACAC
AAGCAAATTTCCCATAGGGCGAAAACGAAAGACAATGAACCAGTGAATTGATGGATGGTGGACCC
ACTCCTTTGGGGTGACATTATC
Done.